could not load library ".../lib/libodbc.so"

I am trying to compile this minimal example package to an app

TestPackage.jl

module TestPackage

using ODBC

function julia_main()::Cint
  try
    @info "Start"
    sleep(3)
    @info "Finish"
  catch exc
    @error "Something went wrong" exception=(exc, catch_backtrace())
    return 1
  end
  return 0
end

end

Project.toml

name = "TestPackage"
uuid = "eff19db2-a3c2-4c04-8788-c5a98477a45c"
authors = ["Jakub Porubcansky <jakub.porubcansky@tangent.works>"]
version = "0.1.0"

[deps]
ODBC = "be6f12e9-ca4f-5eb2-a339-a4f995cc0291"

Manifest.toml

# This file is machine-generated - editing it directly is not advised

julia_version = "1.7.3"
manifest_format = "2.0"

[[deps.ArgTools]]
uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"

[[deps.Artifacts]]
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"

[[deps.Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[deps.ChainRulesCore]]
deps = ["Compat", "LinearAlgebra", "SparseArrays"]
git-tree-sha1 = "80ca332f6dcb2508adba68f22f551adb2d00a624"
uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
version = "1.15.3"

[[deps.ChangesOfVariables]]
deps = ["ChainRulesCore", "LinearAlgebra", "Test"]
git-tree-sha1 = "38f7a08f19d8810338d4f5085211c7dfa5d5bdd8"
uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
version = "0.1.4"

[[deps.Compat]]
deps = ["Dates", "LinearAlgebra", "UUIDs"]
git-tree-sha1 = "924cdca592bc16f14d2f7006754a621735280b74"
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
version = "4.1.0"

[[deps.CompilerSupportLibraries_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"

[[deps.DBInterface]]
git-tree-sha1 = "9b0dc525a052b9269ccc5f7f04d5b3639c65bca5"
uuid = "a10d1c49-ce27-4219-8d33-6db1a4562965"
version = "2.5.0"

[[deps.DataAPI]]
git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40"
uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
version = "1.10.0"

[[deps.DataValueInterfaces]]
git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464"
version = "1.0.0"

[[deps.Dates]]
deps = ["Printf"]
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"

[[deps.DecFP]]
deps = ["DecFP_jll", "Printf", "Random", "SpecialFunctions"]
git-tree-sha1 = "a8269e0a6af8c9d9ae95d15dcfa5628285980cbb"
uuid = "55939f99-70c6-5e9b-8bb0-5071ed7d61fd"
version = "1.3.1"

[[deps.DecFP_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "e9a8da19f847bbfed4076071f6fef8665a30d9e5"
uuid = "47200ebd-12ce-5be5-abb7-8e082af23329"
version = "2.0.3+1"

[[deps.DocStringExtensions]]
deps = ["LibGit2"]
git-tree-sha1 = "5158c2b41018c5f7eb1470d558127ac274eca0c9"
uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
version = "0.9.1"

[[deps.Downloads]]
deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"

[[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"

[[deps.InteractiveUtils]]
deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[deps.InverseFunctions]]
deps = ["Test"]
git-tree-sha1 = "b3364212fb5d870f724876ffcd34dd8ec6d98918"
uuid = "3587e190-3f89-42d0-90ee-14403ec27112"
version = "0.1.7"

[[deps.IrrationalConstants]]
git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151"
uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
version = "0.1.1"

[[deps.IteratorInterfaceExtensions]]
git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
uuid = "82899510-4779-5014-852e-03e436cf321d"
version = "1.0.0"

[[deps.JLLWrappers]]
deps = ["Preferences"]
git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1"
uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
version = "1.4.1"

[[deps.LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"

[[deps.LibCURL_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"

[[deps.LibGit2]]
deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"

[[deps.LibSSH2_jll]]
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"

[[deps.Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"

[[deps.Libiconv_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "42b62845d70a619f063a7da093d995ec8e15e778"
uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
version = "1.16.1+1"

[[deps.LinearAlgebra]]
deps = ["Libdl", "libblastrampoline_jll"]
uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

[[deps.LogExpFunctions]]
deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"]
git-tree-sha1 = "361c2b088575b07946508f135ac556751240091c"
uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
version = "0.3.17"

[[deps.Logging]]
uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"

[[deps.Markdown]]
deps = ["Base64"]
uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"

[[deps.MbedTLS_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"

[[deps.MozillaCACerts_jll]]
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"

[[deps.NetworkOptions]]
uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"

[[deps.ODBC]]
deps = ["DBInterface", "Dates", "DecFP", "Libdl", "Printf", "Random", "Scratch", "Tables", "UUIDs", "Unicode", "iODBC_jll", "unixODBC_jll"]
git-tree-sha1 = "ab457f6208fa4faa5675c81d32275e661a06ad9e"
uuid = "be6f12e9-ca4f-5eb2-a339-a4f995cc0291"
version = "1.1.0"

[[deps.OpenBLAS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"

[[deps.OpenLibm_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "05823500-19ac-5b8b-9628-191a04bc5112"

[[deps.OpenSpecFun_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1"
uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e"
version = "0.5.5+0"

[[deps.OrderedCollections]]
git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.4.1"

[[deps.Pkg]]
deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"

[[deps.Preferences]]
deps = ["TOML"]
git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d"
uuid = "21216c6a-2e73-6563-6e65-726566657250"
version = "1.3.0"

[[deps.Printf]]
deps = ["Unicode"]
uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"

[[deps.REPL]]
deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"

[[deps.Random]]
deps = ["SHA", "Serialization"]
uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

[[deps.SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"

[[deps.Scratch]]
deps = ["Dates"]
git-tree-sha1 = "f94f779c94e58bf9ea243e77a37e16d9de9126bd"
uuid = "6c6a2e73-6563-6170-7368-637461726353"
version = "1.1.1"

[[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"

[[deps.Sockets]]
uuid = "6462fe0b-24de-5631-8697-dd941f90decc"

[[deps.SparseArrays]]
deps = ["LinearAlgebra", "Random"]
uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

[[deps.SpecialFunctions]]
deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d"
uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
version = "2.1.7"

[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"

[[deps.TableTraits]]
deps = ["IteratorInterfaceExtensions"]
git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39"
uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
version = "1.0.1"

[[deps.Tables]]
deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"]
git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1"
uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
version = "1.7.0"

[[deps.Tar]]
deps = ["ArgTools", "SHA"]
uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"

[[deps.Test]]
deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[[deps.UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

[[deps.Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[[deps.Zlib_jll]]
deps = ["Libdl"]
uuid = "83775a58-1f1d-513f-b197-d71354ab007a"

[[deps.iODBC_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "785395fb370d696d98da91eddedbdde18d43b0e3"
uuid = "80337aba-e645-5151-a517-44b13a626b79"
version = "3.52.15+0"

[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl", "OpenBLAS_jll"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"

[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"

[[deps.unixODBC_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg"]
git-tree-sha1 = "228f4299344710cf865b3659c51242ecd238c004"
uuid = "1841a5aa-d9e2-579c-8226-32ed2af93ab1"
version = "2.3.9+0"

To compile the app I run Docker build using the following Dockerfile. The Dockerfile has two stages - in the first one the package is compiled to an app and in the second the app is relocated to a new image without julia installed.

Dockerfile

FROM julia:1.7.3-bullseye AS builder

RUN apt-get update

RUN apt-get -y install \
    build-essential

COPY . TestPackage

RUN julia --project=TestPackage -e "using Pkg; Pkg.instantiate(); Pkg.precompile();"

RUN julia -e "using Pkg; \
              pkg\"add PackageCompiler\"; \
              using PackageCompiler; \
              create_app(\"TestPackage\", \"app\")"

FROM debian:bullseye-slim as runner

RUN apt-get update

COPY --from=builder /app /app

ENTRYPOINT ["/app/bin/TestPackage"]

When running the final image it gives me the following error:

fatal: error thrown and no exception handler available.
InitError(mod=:API, error=ErrorException("could not load library "/root/.julia/artifacts/84637f9dbc8f313838011977325eec613e7ca1bc/lib/libodbc.so"
/root/.julia/artifacts/84637f9dbc8f313838011977325eec613e7ca1bc/lib/libodbc.so: cannot open shared object file: No such file or directory"))
jl_errorf at /buildworker/worker/package_linux64/build/src/rtutils.c:77
jl_load_dynamic_library at /buildworker/worker/package_linux64/build/src/dlload.c:284
jl_get_library_ at /buildworker/worker/package_linux64/build/src/runtime_ccall.cpp:48
jl_get_library_ at /buildworker/worker/package_linux64/build/src/runtime_ccall.cpp:32 [inlined]
jl_load_and_lookup at /buildworker/worker/package_linux64/build/src/runtime_ccall.cpp:61
jlplt_SQLAllocHandle_32126.clone_1 at /app/lib/julia/sys.so (unknown line)
SQLAllocHandle at /root/.julia/packages/ODBC/mjMrW/src/API.jl:91
Handle at /root/.julia/packages/ODBC/mjMrW/src/API.jl:118
Handle at /root/.julia/packages/ODBC/mjMrW/src/API.jl:159 [inlined]
#setupenv#6 at /root/.julia/packages/ODBC/mjMrW/src/API.jl:211
setupenv at /root/.julia/packages/ODBC/mjMrW/src/API.jl:191 [inlined]
__init__ at /root/.julia/packages/ODBC/mjMrW/src/API.jl:233
jfptr___init___32129.clone_1 at /app/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
jl_module_run_initializer at /buildworker/worker/package_linux64/build/src/toplevel.c:73
_finish_julia_init at /buildworker/worker/package_linux64/build/src/init.c:796
julia_init at /buildworker/worker/package_linux64/build/src/init.c:730
jl_init_with_image at /buildworker/worker/package_linux64/build/src/jlapi.c:74
jl_init at /buildworker/worker/package_linux64/build/src/jlapi.c:90
main at /app/bin/TestPackage (unknown line)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
_start at /app/bin/TestPackage (unknown line)

It tries to find the libodbc.so library on a path that does not exist after relocating the app. Does that mean the package is not relocatable? Or am I doing something wrong?

@KristofferC, what's the expectation with PackageCompiler? Should it be bundling required artifacts into the app directory or something? Or is that something the user should do after building the app?

PackageCompiler should bundle everything that is required.

I think the problem here is code like

ODBC.jl/src/API.jl

Line 7 in 88493b6

const unixODBC_inst = unixODBC_jll.libodbcinst

It will store the string to the library at compile time (which nullifies the lookup that jlls do during runtime).

@quinnj Is this something that could be fixed or is there some workaround that I could try?

is there some workaround that I could try?

Remove all the const unixODBC_inst = unixODBC_jll.libodbcinst stuff and just use unixODBC_jll.libodbcinst directly.

Ok, PR that hopefully fixes it: #351

Yes, this fixes it. Thank you very much for a quick action!